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Originally Posted by bethohio3
I'm actually surprised that people care how the files are organized.
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If one wants to be able to use the files outside of Calibre and not store them twice to avoid keeping two locations in sync, I can imagine that this entire issue of Calibre creating its own library can be problematic. This is exactly the case why I never allowed iTunes to organize my files during the time I used an iPod; because I wanted to access the files using other programs, and using the filesystem.
With my books, I don't have this same problem. I use calibre exclusively, because there is no viable alternative, and I don't search for books in the filesystem itself.
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It's taking me a long time to clean up the metadata for my existing books
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Same here. My suggestion would be to polish the metadata into the books. If your library file ever gets corrupted, you can just move your books to another location, make a new library, and re-import the books. The metadata will be re-read.
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If I discover at some point that I wish I had more metadata (different tags, a new hierarchy) then I can add it--and the files don't change at all. I think that's awesome!
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As said above, I poslish the metadata into the books, as it only changes the OPF-file. I'm fine with that. I could get any calibre-specific metadata out of the books using Modify EPUB, should I ever wish to transition to a different program; something which seems unlikely at this point in time. As it stands, with calibre's current feature list and tremendous development pace, it's impossible to catch up to it when starting from scratch. I think that any non-Kovid developed successor to calibre will be a fork.